A Single Nucleotide Polymorphism - SNP is a variation in the DNA sequence occurring commonly within a population (usually >1%). A single nucleotide - A, C, G, or T - in part of the DNA chain differs between two individuals.
For example the diagram shows two DNA fragments for the two individuals. The top sequences in the strands are shown to be:
GATCACAT and GATCGCAT.
Here a single nucleotide is seen to be different: A in the top fragment and G in the one below.
Because the nucleotide sequence along the gene is different, there are now two alleles.

The stretch of the DNA where the SNP is found may be within the coding region of the gene, or the non-coding region of the gene or in the intergenic region i.e. the region between genes.

SNP markers along the genome are used to study the evolutionary processes occurring in bee populations. For example 1136 SNPs were used in the work described in the following article.

In an article entitled Thrice Out of Africa: Ancient and Recent Expansions of the Honey Bee, Apis mellifera
published in 2006, the authors describe a project in which 1136 genotypes from 175 individual from native populations in Europe, Africa, and the Middle East were analyzed using SNPs.
Principle Component Analysis (PCA) showed 4 major clusters which were consistent with those proposed by Ruttner using morphological data: A (Africa), C (Central Europe), M (Western and Northern Europe), and O (Near East).
The data was used to construct a phylogenetic tree.Click here to see the tree as a pop-up. The tree is shown in relationship to the geographical areas occupied by the 4 Groups. Click top left on the map to magnify.
Two features on the map are perhaps surprising regarding Group M:
firstly despite their close geographical proximity Groups M and C are the most distantly related, and
secondly that M was found to be more closely related to A rather than to C or O Groups.
On the basis of these findings the authors proposed that A. mellifera originated in Africa. And that there were subsequently two ancient expansions into Europe by a western route (for M) presumably through the Iberian Peninsular and by an eastern route (for C and O).

However in an article published in 2012 From where did the Western Honeybee (Apis mellifera) originate?
the authors re-evaluated the evidence given in the previous article. They concluded that the hypothesis first proposed by Ruttner involving an expansion from an area close to where the other Apis species are found fits well with the current evidence.